[[!comment format=mdwn
 username="joey"
 subject="""comment 3"""
 date="2017-02-13T20:21:09Z"
 content="""
Thanks for following up with the cause of this.

In fact, assuming you're not using a v6 git-annex repository, it doesn't
really need to update that database at all. But since we'll be upgrading to
v6 eventually, I need to deal with problems like this. Also,
this same problem will also impact the database used for incremental fsck.

I can reproduce this with a v5 repository; dropping a file happens to run a
code path that updates the database. And reproducing it w/o using git-annex too:

	joey@darkstar:~/tmp>mkdir empty
	joey@darkstar:~/tmp>umask
	0002
	joey@darkstar:~/tmp>touch empty/file
	joey@darkstar:~/tmp>sqlite3 empty/db
	SQLite version 3.16.2 2017-01-06 16:32:41
	Enter ".help" for usage hints.
	sqlite> create table foo;
	Error: near ";": syntax error
	sqlite> 
	joey@darkstar:~/tmp>ls -l empty/
	total 0
	-rw-r--r-- 1 joey joey 0 Feb 13 16:33 db
	-rw-rw-r-- 1 joey joey 0 Feb 13 16:32 file

Seems that sqlite uses `0644 & umask` for the db permissions, 
which is *bad* because it doesn't allow the umask to enable the group
write bit. That 0644 is `SQLITE_DEFAULT_FILE_PERMISSIONS`, so it can
be changed to something saner at compile time.

`http://www.sqlite.org/src/doc/trunk/src/os_unix.c` has a useful comment.
Seems that sqlite is careful to make -wal, -journal, and -shm files
have the exact same permissions as main database file.

So, if `.git/annex/keys/*` is updated to have the desired permissions when
the database is created, every further write to the database will keep
using the desired permissions.

Hmm, it turns out that git-annex does already set the database permissions when
creating it, but only if core.sharedRepository is set to group or all. So
there's a workaround; just `git config core.sharedRepository group` when
setting up a repository that's going to be accessed by multiple users. Almost
certianly a better idea than relying on umask anyway; people mess up umask
settings.

I'll go ahead and make it always set sane permissions when creating databases.
I'm not going to try to fix up permissions in existing repositories though.
"""]]